4pnzi-FreeEnergyProtocol.txt

Name

MMGBSA

Software

AMBER11

Parameters

AM1-bcc #atomic charges for ligands
AMBER03 force field
Generalized Amber force field (GAFF)
3 ns
igb = 5

Method

For each ligand, the initial structure was generated with the XDZ_0 method,
as described in the PosePredictionProtocol. Molecular Dynamics simulations and free
energy calculations using MM/GBSA method were conducted to calculate the free energy
of binding. Specifically, the temperature of the prepared complex system was raised
from 0 to 300k in the heating phase. Then, the production phase was performed for 3ns
at a time step of 2 fs. To obtain the free energy of binding, 1500 snapshots were taken
from the last 1.5ns at the 1 ps interval and calculated by implementing the
MM/GBSA method.
Entropical loss during protein-ligand binding was estimated by employing the Nmode module
in the AMBER package based on the 50 snapshots extracted from the last 1.5ns with the 30 ps interval.

4pnzi-PosePredictionProtocol.txt

Name

A template-based method, XDZ_0

Software

OMEGA 2.5/SHAFTS/AMBER11

System Preparation Parameters

maxconfs=500 #OMEGA

System Preparation Method

All the released crystal structures of human
FXR protein-small molecule complexes were collected from the Protein Data Bank.
The co-crystal structures for FXR_1-FXR-36 provided by D3R were also included.
If there exist more than one PDB entries containing identical small molecules
binding to the same pocket, the structure with a higher resolution was kept,
resulting in a total of 62 resulting crystal structures.
Ligand conformational libraries were generated using OMEGA.

Pose Prediction Parameters

AM1-bcc #atomic charges for ligands
AMBER03 force field
Generalized Amber force field (GAFF)

Pose Prediction Method

For a query compound, the SHAFTS program was employed to
calculate its structural similarities (i.e., the shape-feature similarities) with
the small molecules in the released FXR structures. The PDB entry that has the best
similarity score with the query ligand was used as the template.
Then, the query compound was superimposed onto the ligand in the template.
The protein-query compound complex was used as the initial structure for the next
MD refinement with AMBER11. For the compound FXR_10 and FXR_12, co-crystal structures
provided by D3R were used as the initial structures for the following refinement.
Atomic partial charges of each ligand were assigned using
Antechamber based on the AM1-bcc method after ligand minimization. Using the Leap module,
the AMBER03 force field and the Generalized Amber force field (GAFF) were applied to the
receptor and to the ligand, respectively. The hydrogen atoms, water molecules and counter
ions were also added to the complexes. The solvated complexes were then minimized in two steps.
During the first step, the solvent molecules were minimized for 1000 steps via steepest descent,
followed by 3000 steps via conjugate gradient. A 500 kcal/mol/Å^2 restraint was imposed on all
the protein atoms and ligand atoms. During the second step, the protein-ligand complexes and the
solvent were both minimized for 10,000 steps via the steepest descent method, followed by conjugate
gradient minimization until the energy gradient of the system converged to 0.01 kcal/mol/Å.